From Observers to Participants: Joining the Scientific Community

In this essay, we have integrated the voices of our mentors and students to explore 45 years of undergraduate research experiences and their role in shaping our scientific community. In considering our collective experiences, we see undergraduate involvement in research as a rich source of community development, one that has both touched our lives and influenced our teaching

Structural brain correlates of childhood inhibited temperament: an ENIGMA-Anxiety Mega-analysis

NWORubicon 019.201SG.022Pathways through Adolescenc

Cis-regulatory elements in limb development and human congenital malformations

Regulatory elements provide information necessary for the spatial, temporal and dosage appropriate expression of genes. Developmental genes in particular rely on cis-regulatory enhancers to control expression in the various tissues where they are active and cause defects in development. Congenital limb malformations are the second most common class of human birth defects and can be caused both by environmental and genetic factors, and identifying the causal mutation in a patient with an isolated limb malformation is often difficult. The difficulty of identification may be due, in part, to the growing number of cases with isolated limb malformations that are shown to be the result of nucleotide changes in regulatory elements. These regulatory mutations affect gene expression in the developing limb and can cause dramatic changes to patterning, leading to congenital limb malformations. There are multiple examples of mutations in an enhancer known as the zone of polarizing activity regulatory sequence (ZRS) that cause preaxial polydactyly and other malformation phenotypes. The identification of further ZRS mutations along with changes they have to transcription factor binding and resulting phenotypes can help elucidate the mechanisms by which it controls gene expression. While the genes and pathways that determine specific limb signaling centers have been described, the identification of enhancers that determine these centers has been limited. It is possible to identify enhancers that are specific to the zone of polarizing activity (ZPA) and apical ectodermal ridge (AER) signaling centers by isolating these regions. Using H3K27ac ChIP-seq on mouse E11.5 ZPA and AER fluorescently sorted cells, I identified thousands of specific signaling center enhancers. Mouse transgenic assays confirmed that several of them function as ZPA and AER enhancers. Combined, these results provide novel ZPA and AER enhancers that may play important roles in limb development. Because the ZPA and AER have critical roles in establishing the three axes and patterning the limb, changes in enhancer function can result in malformations of limb structures

Human developmental enhancers conserved between deuterostomes and protostomes.

The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores). Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow

A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre‐axial polydactyly, post‐axial polydactyly, and syndactyly

Limb malformations are one of the most common types of human congenital malformations. Mutations in the ZRS enhancer of Sonic Hedgehog are thought to be responsible for pre-axial polydactyly in multiple independent families. Here, we describe a large Balochi tribal family from Southern Punjab, Pakistan, with a variable set of limb malformations and a novel ZRS mutation. The family has a limb phenotype characterized by triphalangeal thumb, pre-axial polydactyly, and post-axial polydactyly. There is also a high degree of phenotypic heterogeneity with less common clinical findings in the affected family members that include osseous syndactyly of forth-fifth fingers, clinodactyly, hypoplasia of mesoaxial fingers, and bifid halluces. The presentation in most of the affected patients was bilateral and symmetrical. A heterozygous C>A mutation at position 287 of the ZRS enhancer (chr7:156,584,283; hg19) was detected in all affected subjects and is absent from four unaffected family members, 42 unrelated samples, and multiple databases of human variation. Combined, these results identify a novel ZRS287 C>A mutation which leads to a variable spectrum of limb phenotypes

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

<div><p>The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores). Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.</p> </div

Ancient enhancers.

<p>(A) Pattern of conservation of Bicores across the metazoan tree. Green checks denote conservation of sequence and gene synteny. Red crosses denote no detectable sequence conservation. (B) Characteristics of Bicores. CNS – central nervous system.</p

Total number of bases (coding versus conserved non-coding) in human that align to each species.

<p>Species are ordered at progressively greater evolutionary distances. Placental mammal CNEs – placental mammal conserved non-coding elements.</p

Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.

Nonsense mutations in FGF16 have recently been linked to X-linked recessive hand malformations with fusion between the fourth and the fifth metacarpals and hypoplasia of the fifth digit (MF4; MIM#309630). The purpose of this study was to perform careful clinical phenotyping and to define molecular mechanisms behind X-linked recessive MF4 in three unrelated families. We performed whole-exome sequencing, and identified three novel mutations in FGF16. The functional impact of FGF16 loss was further studied using morpholino-based suppression of fgf16 in zebrafish. In addition, clinical investigations revealed reduced penetrance and variable expressivity of the MF4 phenotype. Cardiac disorders, including myocardial infarction and atrial fibrillation followed the X-linked FGF16 mutated trait in one large family. Our findings establish that a mutation in exon 1, 2 or 3 of FGF16 results in X-linked recessive MF4 and expand the phenotypic spectrum of FGF16 mutations to include a possible correlation with heart disease